This package provides an R implementation of ROMA. The package is under active development and is currently being tested.
A Java implementation developed by Andrei Zynovyev and is also available.
The rRoma package relies on the scater package, which is available only on BioConductor. This package can be installed with the following command
source("https://bioconductor.org/biocLite.R")
biocLite("scater")
rRoma can then be installed using devtools
if(!require("devtools")){
install.packages("devtools")
}
devtools::install_github("Albluca/rROMA")
The packages GEOquery, tictoc, and readr are not required to run rROMA, but are used in the following example and need to be installed to reproduce the analysis
if(!require("GEOquery")){
source("https://bioconductor.org/biocLite.R")
biocLite("GEOquery")
}
## Loading required package: GEOquery
## Loading required package: Biobase
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
##
## IQR, mad, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, cbind, colnames,
## do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff,
## sort, table, tapply, union, unique, unsplit, which, which.max,
## which.min
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
if(!require("readr")){
install.packages("readr")
}
## Loading required package: readr
if(!require("tictoc")){
install.packages("tictoc")
}
## Loading required package: tictoc
The package can be loaded with the usual syntax, i.e., by typing
library(rRoma)
rRoma requires a gene expression matrix - with column names indicating samples and row names indicating gene names - and a module file containing information on the genesets that need to be evaluated. The module file can be loaded from a GMT file. Functions to automate the generation of then GMT file are also available.
Various functions are then available to explore the analysis, including plotting and statistical cross sample analysis.
To show a concrete example of rROMA we will use a dataset available on GEO. The output of the analysis is not reported due to limitation in the markdown files used by GitHub. Let us begin by getting the description of the dataset
library(GEOquery)
gse <- getGEO("GSE50760", GSEMatrix = TRUE)
## https://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50760/matrix/
## OK
## Found 1 file(s)
## GSE50760_series_matrix.txt.gz
## File stored at:
## /var/folders/0d/46tymjcj0qxbtqgvxp1623400000gn/T//RtmpVCDhTg/GPL11154.soft
Then we get the actual expression expression files
filePaths = getGEOSuppFiles("GSE50760")
## https://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50760/suppl/
## OK
Now we can construct the expression matrix. Note that the code below is designed to work on a Unix-like environment (e.g. MacOS). The execution on a Windows environment may require replacing "/" with "\".
library(readr)
Content <- untar(row.names(filePaths)[1], list = TRUE)
untar(row.names(filePaths)[1], list = FALSE)
MatData <- NULL
for(i in 1:length(Content)){
Exp <- read_delim(Content[i], "\t", escape_double = FALSE, trim_ws = TRUE)
if(is.null(MatData)){
MatData <- cbind(unlist(Exp[,1]), unlist(Exp[,2]))
} else {
if(any(MatData[,1] != unlist(Exp[,1]))){
stop("Incompatible samples")
}
MatData <- cbind(MatData, unlist(Exp[,2]))
}
file.remove(Content[i])
}
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_2.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_3.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_5.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_6.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_7.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_8.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_9.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_10.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_12.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_13.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_17.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_18.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_19.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_20.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_21.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_22.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_23.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_24.1_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_2.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_3.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_5.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_6.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_7.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_8.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_9.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_10.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_12.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_13.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_17.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_18.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_19.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_20.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_21.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_22.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_23.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_24.2_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_2.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_3.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_5.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_6.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_7.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_8.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_9.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_10.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_12.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_13.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_17.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_18.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_19.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_20.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_21.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_22.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_23.3_FPKM = col_double()
## )
## Parsed with column specification:
## cols(
## genes = col_character(),
## AMC_24.3_FPKM = col_double()
## )
SplitPath <- unlist(strsplit(rownames(filePaths)[1], "/"))
SplitPath <- SplitPath[-length(SplitPath)]
unlink(x = paste(SplitPath, collapse = "/"), recursive = TRUE)
Genes <- MatData[,1]
MatData <- data.matrix(data.frame(MatData[,-1]))
rownames(MatData) <- Genes
colnames(MatData) <- unlist(lapply(strsplit(Content, "_"), "[[", 1))
And look at the different groups of cells present
Type <- as.character(gse$GSE50760_series_matrix.txt.gz[[1]])
Type <- unlist(lapply(strsplit(Type, " "), "[[", 1))
names(Type) = as.character(gse$GSE50760_series_matrix.txt.gz[[2]])
table(Type)
## Type
## metastasized normal primary
## 18 18 18
For convenience, we will transform Type into a factor:
Type <- as.factor(Type)
At this point we can create the metagene files. We will extract all the “HALLPARK” geneset from MSig.
AllHall <- SelectFromMSIGdb("HALLMARK")
## [1] "Searching in MsigDB v6.0"
AllHall <- lapply(AllHall, function(x){
x$Name <- sub("HALLMARK_", "", x$Name)
x
})
To reduce potential problmes we will remove genes with a duplicated name
if(any(duplicated(rownames(MatData)))){
MatData <- MatData[!(rownames(MatData) %in% rownames(MatData)[duplicated(rownames(MatData))]), ]
}
And now we are ready to perform ROMA without fixed center
tictoc::tic()
Data.NFC <- rRoma.R(ExpressionMatrix = MatData, centerData = TRUE, ExpFilter = FALSE,
ApproxSamples = 5, ModuleList = AllHall, MinGenes = 10,
MaxGenes = 200, nSamples = 100, UseWeigths = FALSE,
DefaultWeight = 1, FixedCenter = FALSE,
GeneOutDetection = 'L1OutExpOut', GeneOutThr = 5,
GeneSelMode = "All", SampleFilter = TRUE, MoreInfo = FALSE,
PlotData = FALSE, PCSignMode = "CorrelateAllWeightsByGene", OutGeneNumber = 5,
Ncomp = 100, OutGeneSpace = 5, PCADims = 2, PCSignThr = NULL,
UseParallel = TRUE, nCores = 3, ClusType = "FORK", FullSampleInfo = FALSE)
## [1] "Centering gene expression over samples"
## [1] "Using local center (NOT centering over genes)"
## [1] "All the genesets will be used"
## [1] "2017-04-12 16:59:47 CEST"
## [1] "[1/50] Working on NOTCH_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_NOTCH_SIGNALING"
## [1] "32 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "KAT2A"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.218112782355521 L1/L2 = 2.14223137940078"
## [1] "Median expression (uncentered): 11705.5"
## [1] "Median expression (centered/weighted): -55.4722222222217"
## [1] "Post-filter data"
## [1] "L1 = 0.200047778345952 L1/L2 = 1.87427068873295"
## [1] "Median expression (uncentered): 11760.5"
## [1] "Median expression (centered/weighted): -8.19444444444434"
## [1] "Previous sample size: 0"
## [1] "Next sample size: 32"
## [1] "Computing samples"
## user system elapsed
## 0.047 0.027 6.832
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 16:59:57 CEST"
## [1] "[2/50] Working on HEDGEHOG_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HEDGEHOG_SIGNALING"
## [1] "36 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "SHH" "SCG2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.238951393021584 L1/L2 = 2.20609876528576"
## [1] "Median expression (uncentered): 9107"
## [1] "Median expression (centered/weighted): -230.555555555556"
## [1] "Post-filter data"
## [1] "L1 = 0.19044828278847 L1/L2 = 1.59121559698214"
## [1] "Median expression (uncentered): 9113"
## [1] "Median expression (centered/weighted): -230.555555555556"
## [1] "Previous sample size: 32"
## [1] "Next sample size: 36"
## [1] "Computing samples"
## user system elapsed
## 0.049 0.028 2.672
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:00 CEST"
## [1] "[3/50] Working on ANGIOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ANGIOGENESIS"
## [1] "36 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "SERPINA5" "OLR1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.241722268030935 L1/L2 = 2.07659291489548"
## [1] "Median expression (uncentered): 9486.5"
## [1] "Median expression (centered/weighted): -524.962962962964"
## [1] "Post-filter data"
## [1] "L1 = 0.198532563319471 L1/L2 = 1.72706137414067"
## [1] "Median expression (uncentered): 9719.5"
## [1] "Median expression (centered/weighted): -463.740740740741"
## [1] "Previous sample size: 36"
## [1] "Next sample size: 36"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:00 CEST"
## [1] "[4/50] Working on PANCREAS_BETA_CELLS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PANCREAS_BETA_CELLS"
## [1] "40 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "SYT13" "SCGN" "SST"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.432865048299536 L1/L2 = 5.11128199148605"
## [1] "Median expression (uncentered): 5991.5"
## [1] "Median expression (centered/weighted): -116.222222222222"
## [1] "Post-filter data"
## [1] "L1 = 0.393073511213135 L1/L2 = 3.93665656795046"
## [1] "Median expression (uncentered): 5600"
## [1] "Median expression (centered/weighted): -106.592592592593"
## [1] "Previous sample size: 36"
## [1] "Next sample size: 40"
## [1] "Computing samples"
## user system elapsed
## 0.052 0.028 3.002
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:03 CEST"
## [1] "[5/50] Working on WNT_BETA_CATENIN_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_WNT_BETA_CATENIN_SIGNALING"
## [1] "42 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.204800119038035 L1/L2 = 2.05763805284028"
## [1] "Median expression (uncentered): 10239"
## [1] "Median expression (centered/weighted): -323.583333333333"
## [1] "Post-filter data"
## [1] "L1 = 0.204800119038035 L1/L2 = 2.05763805284033"
## [1] "Median expression (uncentered): 10239"
## [1] "Median expression (centered/weighted): -323.583333333333"
## [1] "Previous sample size: 40"
## [1] "Next sample size: 42"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:03 CEST"
## [1] "[6/50] Working on APICAL_SURFACE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APICAL_SURFACE"
## [1] "44 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.274912143216074 L1/L2 = 3.11817850117445"
## [1] "Median expression (uncentered): 8648"
## [1] "Median expression (centered/weighted): -75.9444444444444"
## [1] "Post-filter data"
## [1] "L1 = 0.274912143216074 L1/L2 = 3.11817850097864"
## [1] "Median expression (uncentered): 8648"
## [1] "Median expression (centered/weighted): -75.9444444444444"
## [1] "Previous sample size: 40"
## [1] "Next sample size: 44"
## [1] "Computing samples"
## user system elapsed
## 0.057 0.031 3.583
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:07 CEST"
## [1] "[7/50] Working on REACTIVE_OXIGEN_SPECIES_PATHWAY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY"
## [1] "48 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181146251389831 L1/L2 = 1.73973885217875"
## [1] "Median expression (uncentered): 12683.5"
## [1] "Median expression (centered/weighted): 25.75"
## [1] "Post-filter data"
## [1] "L1 = 0.181146251389831 L1/L2 = 1.73973885217861"
## [1] "Median expression (uncentered): 12683.5"
## [1] "Median expression (centered/weighted): 25.75"
## [1] "Previous sample size: 44"
## [1] "Next sample size: 48"
## [1] "Computing samples"
## user system elapsed
## 0.059 0.030 4.130
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:11 CEST"
## [1] "[8/50] Working on TGF_BETA_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TGF_BETA_SIGNALING"
## [1] "54 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.165381028156573 L1/L2 = 2.00084563303275"
## [1] "Median expression (uncentered): 12778"
## [1] "Median expression (centered/weighted): 111.148148148148"
## [1] "Post-filter data"
## [1] "L1 = 0.165381028156573 L1/L2 = 2.0008456330748"
## [1] "Median expression (uncentered): 12778"
## [1] "Median expression (centered/weighted): 111.148148148148"
## [1] "Previous sample size: 48"
## [1] "Next sample size: 54"
## [1] "Computing samples"
## user system elapsed
## 0.059 0.030 4.456
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:15 CEST"
## [1] "[9/50] Working on MYC_TARGETS_V2 - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYC_TARGETS_V2"
## [1] "58 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.304531039739229 L1/L2 = 3.3022126460369"
## [1] "Median expression (uncentered): 11774.5"
## [1] "Median expression (centered/weighted): 72.2037037037035"
## [1] "Post-filter data"
## [1] "L1 = 0.304531039739229 L1/L2 = 3.30221264603692"
## [1] "Median expression (uncentered): 11774.5"
## [1] "Median expression (centered/weighted): 72.2037037037035"
## [1] "Previous sample size: 54"
## [1] "Next sample size: 58"
## [1] "Computing samples"
## user system elapsed
## 0.061 0.030 5.368
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:21 CEST"
## [1] "[10/50] Working on CHOLESTEROL_HOMEOSTASIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_CHOLESTEROL_HOMEOSTASIS"
## [1] "74 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "ADH4" "CTNNB1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.141170520941401 L1/L2 = 1.77967329977645"
## [1] "Median expression (uncentered): 12220"
## [1] "Median expression (centered/weighted): 55.75"
## [1] "Post-filter data"
## [1] "L1 = 0.125574406969829 L1/L2 = 1.5376947832314"
## [1] "Median expression (uncentered): 12324.5"
## [1] "Median expression (centered/weighted): 69.6296296296296"
## [1] "Previous sample size: 58"
## [1] "Next sample size: 74"
## [1] "Computing samples"
## user system elapsed
## 0.063 0.030 7.336
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:29 CEST"
## [1] "[11/50] Working on IL6_JAK_STAT3_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_IL6_JAK_STAT3_SIGNALING"
## [1] "87 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "CNTFR"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.140526203004054 L1/L2 = 1.0802523311964"
## [1] "Median expression (uncentered): 11083"
## [1] "Median expression (centered/weighted): -62.8333333333333"
## [1] "Post-filter data"
## [1] "L1 = 0.133721296466459 L1/L2 = 1.00687921369759"
## [1] "Median expression (uncentered): 11113.5"
## [1] "Median expression (centered/weighted): -62.8333333333333"
## [1] "Previous sample size: 74"
## [1] "Next sample size: 87"
## [1] "Computing samples"
## user system elapsed
## 0.070 0.032 9.432
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:38 CEST"
## [1] "[12/50] Working on PROTEIN_SECRETION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PROTEIN_SECRETION"
## [1] "96 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "COG2" "SSPN"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.134342256557168 L1/L2 = 1.50640841910325"
## [1] "Median expression (uncentered): 11815.5"
## [1] "Median expression (centered/weighted): -85.4074074074069"
## [1] "Post-filter data"
## [1] "L1 = 0.120722324899839 L1/L2 = 1.36322507276574"
## [1] "Median expression (uncentered): 11813"
## [1] "Median expression (centered/weighted): -87.240740740741"
## [1] "Previous sample size: 87"
## [1] "Next sample size: 96"
## [1] "Computing samples"
## user system elapsed
## 0.077 0.034 11.907
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:50 CEST"
## [1] "[13/50] Working on INTERFERON_ALPHA_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INTERFERON_ALPHA_RESPONSE"
## [1] "97 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "SAMD9L" "IL7"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.124076927298751 L1/L2 = 1.26105293109549"
## [1] "Median expression (uncentered): 11800.5"
## [1] "Median expression (centered/weighted): 73.333333333333"
## [1] "Post-filter data"
## [1] "L1 = 0.110491733289259 L1/L2 = 1.09630025994044"
## [1] "Median expression (uncentered): 11805"
## [1] "Median expression (centered/weighted): 48.3148148148157"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 97"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:51 CEST"
## [1] "[14/50] Working on ANDROGEN_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ANDROGEN_RESPONSE"
## [1] "101 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "TARP" "KRT8" "PTPN21"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.173331867964937 L1/L2 = 2.05229451754152"
## [1] "Median expression (uncentered): 11686.5"
## [1] "Median expression (centered/weighted): -13.4629629629631"
## [1] "Post-filter data"
## [1] "L1 = 0.148682861472385 L1/L2 = 1.6979588768767"
## [1] "Median expression (uncentered): 11701.5"
## [1] "Median expression (centered/weighted): -6.02777777777781"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 101"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:00:51 CEST"
## [1] "[15/50] Working on PEROXISOME - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PEROXISOME"
## [1] "103 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "FABP6" "CEL"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.177410220658441 L1/L2 = 2.33195718444532"
## [1] "Median expression (uncentered): 11493"
## [1] "Median expression (centered/weighted): 9.24074074074088"
## [1] "Post-filter data"
## [1] "L1 = 0.159595634840205 L1/L2 = 2.04648139430166"
## [1] "Median expression (uncentered): 11537.5"
## [1] "Median expression (centered/weighted): 21.1481481481478"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 103"
## [1] "Computing samples"
## user system elapsed
## 0.093 0.037 14.731
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:06 CEST"
## [1] "[16/50] Working on PI3K_AKT_MTOR_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PI3K_AKT_MTOR_SIGNALING"
## [1] "105 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "4 genes will be filtered:"
## [1] "PLCG1" "CDK2" "PRKCB" "PITX2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181268760922922 L1/L2 = 2.28063761954279"
## [1] "Median expression (uncentered): 11434"
## [1] "Median expression (centered/weighted): -27.037037037037"
## [1] "Post-filter data"
## [1] "L1 = 0.149686406557347 L1/L2 = 1.74996481657705"
## [1] "Median expression (uncentered): 11462.5"
## [1] "Median expression (centered/weighted): -27.037037037037"
## [1] "Previous sample size: 103"
## [1] "Next sample size: 105"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:07 CEST"
## [1] "[17/50] Working on UNFOLDED_PROTEIN_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UNFOLDED_PROTEIN_RESPONSE"
## [1] "112 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "NOP14" "STC2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.21406859847449 L1/L2 = 3.34151977510639"
## [1] "Median expression (uncentered): 12035"
## [1] "Median expression (centered/weighted): 5.38888888888869"
## [1] "Post-filter data"
## [1] "L1 = 0.187841032620879 L1/L2 = 2.85900544694751"
## [1] "Median expression (uncentered): 12041"
## [1] "Median expression (centered/weighted): 5.38888888888869"
## [1] "Previous sample size: 103"
## [1] "Next sample size: 112"
## [1] "Computing samples"
## user system elapsed
## 0.096 0.037 21.404
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:29 CEST"
## [1] "[18/50] Working on BILE_ACID_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_BILE_ACID_METABOLISM"
## [1] "112 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "11 genes will be filtered:"
## [1] "AKR1D1" "CYP8B1" "SLC27A5" "AGXT" "PIPOX" "HAO1" "AQP9"
## [8] "ALDH8A1" "GNMT" "DIO1" "GC"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.274715196168859 L1/L2 = 2.5176151480751"
## [1] "Median expression (uncentered): 10112.5"
## [1] "Median expression (centered/weighted): -149.046296296296"
## [1] "Post-filter data"
## [1] "L1 = 0.169762551957633 L1/L2 = 1.47194143071892"
## [1] "Median expression (uncentered): 10745.5"
## [1] "Median expression (centered/weighted): -36.9537037037039"
## [1] "Previous sample size: 112"
## [1] "Next sample size: 112"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:29 CEST"
## [1] "[19/50] Working on SPERMATOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_SPERMATOGENESIS"
## [1] "133 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "17 genes will be filtered:"
## [1] "PHF7" "YBX2" "CSNK2A2" "MLF1" "CLPB" "RPL39L" "CHFR"
## [8] "NEK2" "DBF4" "TTK" "NCAPH" "SCG5" "TLE4" "STRBP"
## [15] "MEP1B" "GFI1" "IP6K1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.200177635712892 L1/L2 = 2.47889329777171"
## [1] "Median expression (uncentered): 5053"
## [1] "Median expression (centered/weighted): -14.3703703703704"
## [1] "Post-filter data"
## [1] "L1 = 0.159071132641927 L1/L2 = 1.79944760493907"
## [1] "Median expression (uncentered): 3985"
## [1] "Median expression (centered/weighted): -14.3703703703704"
## [1] "Previous sample size: 112"
## [1] "Next sample size: 133"
## [1] "Computing samples"
## user system elapsed
## 0.109 0.040 26.114
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:56 CEST"
## [1] "[20/50] Working on COAGULATION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_COAGULATION"
## [1] "137 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "18 genes will be filtered:"
## [1] "F2" "PLG" "F9" "PROZ" "F11" "MBL2"
## [7] "F13B" "MASP2" "C8A" "C8B" "C9" "SERPINC1"
## [13] "ITIH1" "KLKB1" "TF" "HRG" "CPN1" "CPB2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.323430575157779 L1/L2 = 3.16191642872064"
## [1] "Median expression (uncentered): 10678"
## [1] "Median expression (centered/weighted): -461.537037037037"
## [1] "Post-filter data"
## [1] "L1 = 0.192217204020216 L1/L2 = 1.89573704417201"
## [1] "Median expression (uncentered): 11361"
## [1] "Median expression (centered/weighted): -212.768518518519"
## [1] "Previous sample size: 133"
## [1] "Next sample size: 137"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:01:56 CEST"
## [1] "[21/50] Working on UV_RESPONSE_DN - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UV_RESPONSE_DN"
## [1] "144 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "LPAR1" "PTPN21" "PRKAR2B" "KCNMA1" "KIT"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.179342830009261 L1/L2 = 2.49233698976675"
## [1] "Median expression (uncentered): 11625.5"
## [1] "Median expression (centered/weighted): 39.8240740740741"
## [1] "Post-filter data"
## [1] "L1 = 0.136384678924822 L1/L2 = 1.77642311915537"
## [1] "Median expression (uncentered): 11625.5"
## [1] "Median expression (centered/weighted): 38.4537037037035"
## [1] "Previous sample size: 133"
## [1] "Next sample size: 144"
## [1] "Computing samples"
## user system elapsed
## 0.119 0.045 26.587
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:02:24 CEST"
## [1] "[22/50] Working on DNA_REPAIR - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_DNA_REPAIR"
## [1] "149 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "POLR2D" "RFC2" "RPA3" "TH1L" "USP11" "FEN1" "CCNO"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.182895432381036 L1/L2 = 2.54676704245772"
## [1] "Median expression (uncentered): 12151.5"
## [1] "Median expression (centered/weighted): 2.87037037037044"
## [1] "Post-filter data"
## [1] "L1 = 0.142135649623414 L1/L2 = 1.81503583223052"
## [1] "Median expression (uncentered): 12162.5"
## [1] "Median expression (centered/weighted): 3.75"
## [1] "Previous sample size: 144"
## [1] "Next sample size: 149"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:02:24 CEST"
## [1] "[23/50] Working on FATTY_ACID_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_FATTY_ACID_METABOLISM"
## [1] "158 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "CYP4A11" "HAO2" "RDH16" "TDO2" "CPOX"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.180473177147369 L1/L2 = 2.33251497309967"
## [1] "Median expression (uncentered): 11697"
## [1] "Median expression (centered/weighted): -61.1111111111113"
## [1] "Post-filter data"
## [1] "L1 = 0.159735964178936 L1/L2 = 2.39116233571903"
## [1] "Median expression (uncentered): 11778"
## [1] "Median expression (centered/weighted): -27.8611111111113"
## [1] "Previous sample size: 144"
## [1] "Next sample size: 158"
## [1] "Computing samples"
## user system elapsed
## 0.128 0.041 30.009
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:02:55 CEST"
## [1] "[24/50] Working on UV_RESPONSE_UP - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UV_RESPONSE_UP"
## [1] "158 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "ATP6V1C1" "NUPL1" "CDK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181058788062094 L1/L2 = 2.90008533189139"
## [1] "Median expression (uncentered): 11631"
## [1] "Median expression (centered/weighted): -11.9907407407409"
## [1] "Post-filter data"
## [1] "L1 = 0.165656289260666 L1/L2 = 2.57870576074635"
## [1] "Median expression (uncentered): 11625"
## [1] "Median expression (centered/weighted): -13.8333333333334"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 158"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:02:56 CEST"
## [1] "[25/50] Working on APOPTOSIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APOPTOSIS"
## [1] "161 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "CDK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.168611837463739 L1/L2 = 2.81382680332351"
## [1] "Median expression (uncentered): 11603.5"
## [1] "Median expression (centered/weighted): -98.8703703703704"
## [1] "Post-filter data"
## [1] "L1 = 0.164031679111937 L1/L2 = 2.71011909845197"
## [1] "Median expression (uncentered): 11606.5"
## [1] "Median expression (centered/weighted): -96.3425925925922"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 161"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:02:57 CEST"
## [1] "[26/50] Working on ADIPOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ADIPOGENESIS"
## [1] "197 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "4 genes will be filtered:"
## [1] "FABP4" "SSPN" "ITIH5" "SNCG"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.177918510194237 L1/L2 = 2.91107986716666"
## [1] "Median expression (uncentered): 11826.5"
## [1] "Median expression (centered/weighted): -52.1111111111113"
## [1] "Post-filter data"
## [1] "L1 = 0.160074308769207 L1/L2 = 2.65037577827351"
## [1] "Median expression (uncentered): 11837.5"
## [1] "Median expression (centered/weighted): -57.8703703703704"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 197"
## [1] "Computing samples"
## user system elapsed
## 0.146 0.042 44.794
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:43 CEST"
## [1] "[27/50] Working on COMPLEMENT - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_COMPLEMENT"
## [1] "198 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "F5" "F7" "PLG" "KLKB1" "F2" "OLR1"
## [7] "C9" "SERPINC1" "APOA4" "ITIH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.177212990024261 L1/L2 = 2.0653273934645"
## [1] "Median expression (uncentered): 11150"
## [1] "Median expression (centered/weighted): -63.2500000000005"
## [1] "Post-filter data"
## [1] "L1 = 0.136783170017269 L1/L2 = 1.55119273727985"
## [1] "Median expression (uncentered): 11345"
## [1] "Median expression (centered/weighted): 8.36111111111131"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 198"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:44 CEST"
## [1] "[28/50] Working on HEME_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HEME_METABOLISM"
## [1] "198 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "CPOX" "TRAK2" "KAT2B" "HDGF" "SLC30A10" "DARC"
## [7] "CDR2" "ABCG2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.197947362207264 L1/L2 = 3.11930749203142"
## [1] "Median expression (uncentered): 10907.5"
## [1] "Median expression (centered/weighted): -54.75"
## [1] "Post-filter data"
## [1] "L1 = 0.157900910332656 L1/L2 = 2.44265373607207"
## [1] "Median expression (uncentered): 10909.5"
## [1] "Median expression (centered/weighted): -53.8148148148146"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 198"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:45 CEST"
## [1] "[29/50] Working on MITOTIC_SPINDLE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MITOTIC_SPINDLE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "KIF23" "CKAP5" "TTK" "KIF4A" "ESPL1" "CENPF" "KIF20B"
## [8] "DLGAP5" "SMC1A" "SMC4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.196428373056914 L1/L2 = 1.95848782996468"
## [1] "Median expression (uncentered): 11343.5"
## [1] "Median expression (centered/weighted): -68.2870370370365"
## [1] "Post-filter data"
## [1] "L1 = 0.15738206537971 L1/L2 = 1.69734730299492"
## [1] "Median expression (uncentered): 11373.5"
## [1] "Median expression (centered/weighted): -74.7592592592591"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:47 CEST"
## [1] "[30/50] Working on INTERFERON_GAMMA_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INTERFERON_GAMMA_RESPONSE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "CASP7" "KLRK1" "IL7" "SSPN" "NUP93" "IRF4" "P2RY14"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.150157131609852 L1/L2 = 1.51633570468931"
## [1] "Median expression (uncentered): 11584.5"
## [1] "Median expression (centered/weighted): 52.0185185185182"
## [1] "Post-filter data"
## [1] "L1 = 0.11987858402575 L1/L2 = 1.15502490917538"
## [1] "Median expression (uncentered): 11603.5"
## [1] "Median expression (centered/weighted): 52.0185185185182"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:48 CEST"
## [1] "[31/50] Working on E2F_TARGETS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_E2F_TARGETS"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "DSCC1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.314770741889393 L1/L2 = 3.60291709370035"
## [1] "Median expression (uncentered): 12250.5"
## [1] "Median expression (centered/weighted): 26.4166666666661"
## [1] "Post-filter data"
## [1] "L1 = 0.308534543835881 L1/L2 = 3.49096292351753"
## [1] "Median expression (uncentered): 12255.5"
## [1] "Median expression (centered/weighted): 27.0925925925922"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:49 CEST"
## [1] "[32/50] Working on MYC_TARGETS_V1 - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYC_TARGETS_V1"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "SSBP1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.270877044420821 L1/L2 = 4.25325830465217"
## [1] "Median expression (uncentered): 13016"
## [1] "Median expression (centered/weighted): -15.1388888888896"
## [1] "Post-filter data"
## [1] "L1 = 0.265540480253548 L1/L2 = 4.12059732705815"
## [1] "Median expression (uncentered): 13016"
## [1] "Median expression (centered/weighted): -15.1388888888896"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:50 CEST"
## [1] "[33/50] Working on INFLAMMATORY_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INFLAMMATORY_RESPONSE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "AQP9" "INHBA" "BDKRB1" "OLR1" "PTGER2" "LPAR1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.208197161544327 L1/L2 = 2.13866407915465"
## [1] "Median expression (uncentered): 9834.5"
## [1] "Median expression (centered/weighted): -114.222222222222"
## [1] "Post-filter data"
## [1] "L1 = 0.180442998473296 L1/L2 = 1.77189580487971"
## [1] "Median expression (uncentered): 9893"
## [1] "Median expression (centered/weighted): -103.62037037037"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:51 CEST"
## [1] "[34/50] Working on XENOBIOTIC_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_XENOBIOTIC_METABOLISM"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "18 genes will be filtered:"
## [1] "CYP1A2" "FMO3" "SLC22A1" "ARG1" "UPB1" "HGFAC" "F11"
## [8] "GNMT" "GCKR" "PLG" "VTN" "HRG" "IGFBP1" "TAT"
## [15] "MBL2" "ANGPTL3" "CYP2E1" "ITIH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.292807440948799 L1/L2 = 3.70273205264898"
## [1] "Median expression (uncentered): 11196"
## [1] "Median expression (centered/weighted): -146.101851851852"
## [1] "Post-filter data"
## [1] "L1 = 0.170060422811155 L1/L2 = 1.92535385283345"
## [1] "Median expression (uncentered): 11514"
## [1] "Median expression (centered/weighted): -50.0648148148151"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:52 CEST"
## [1] "[35/50] Working on GLYCOLYSIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_GLYCOLYSIS"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "PRPS1" "NANP" "STC2" "MET" "STC1" "KIF20A" "CAPN5"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.187881288445727 L1/L2 = 2.98541775505528"
## [1] "Median expression (uncentered): 11560.5"
## [1] "Median expression (centered/weighted): -71.1759259259254"
## [1] "Post-filter data"
## [1] "L1 = 0.155959047132592 L1/L2 = 2.41909861887286"
## [1] "Median expression (uncentered): 11576.5"
## [1] "Median expression (centered/weighted): -63.5000000000002"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:53 CEST"
## [1] "[36/50] Working on KRAS_SIGNALING_DN - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_KRAS_SIGNALING_DN"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "15 genes will be filtered:"
## [1] "SPTBN2" "SIDT1" "CLDN8" "THRB" "SERPINA10"
## [6] "PRODH" "EDN2" "INSL5" "UGT2B17" "SLC6A14"
## [11] "GP2" "SLC38A3" "ITIH3" "CNTFR" "SPHK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.229182701054158 L1/L2 = 2.88938438925108"
## [1] "Median expression (uncentered): 3568"
## [1] "Median expression (centered/weighted): -136.481481481481"
## [1] "Post-filter data"
## [1] "L1 = 0.175487049850585 L1/L2 = 2.03391006868511"
## [1] "Median expression (uncentered): 3335"
## [1] "Median expression (centered/weighted): -105.157407407408"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:55 CEST"
## [1] "[37/50] Working on TNFA_SIGNALING_VIA_NFKB - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TNFA_SIGNALING_VIA_NFKB"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "FOSL1" "SERPINE1" "TNFAIP6" "INHBA" "OLR1" "FJX1"
## [7] "DUSP4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.162947244753867 L1/L2 = 2.56758093294394"
## [1] "Median expression (uncentered): 11567.5"
## [1] "Median expression (centered/weighted): -10.064814814815"
## [1] "Post-filter data"
## [1] "L1 = 0.131221002110508 L1/L2 = 1.95834317443366"
## [1] "Median expression (uncentered): 11665.5"
## [1] "Median expression (centered/weighted): 23.5925925925922"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:56 CEST"
## [1] "[38/50] Working on HYPOXIA - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HYPOXIA"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "11 genes will be filtered:"
## [1] "SERPINE1" "STC1" "STC2" "WISP2" "EDN2" "KLF7"
## [7] "B4GALNT2" "PPARGC1A" "BCL2" "GCNT2" "SRPX"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.191690372496674 L1/L2 = 3.23228285595165"
## [1] "Median expression (uncentered): 11261"
## [1] "Median expression (centered/weighted): -120.083333333333"
## [1] "Post-filter data"
## [1] "L1 = 0.141630057600327 L1/L2 = 2.35025967160801"
## [1] "Median expression (uncentered): 11331.5"
## [1] "Median expression (centered/weighted): -105.416666666667"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:57 CEST"
## [1] "[39/50] Working on G2M_CHECKPOINT - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_G2M_CHECKPOINT"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "KIF4A" "ORC6"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.29123648386556 L1/L2 = 3.21606861912669"
## [1] "Median expression (uncentered): 11853"
## [1] "Median expression (centered/weighted): -69.8240740740739"
## [1] "Post-filter data"
## [1] "L1 = 0.277594300097032 L1/L2 = 3.00008230311599"
## [1] "Median expression (uncentered): 11853.5"
## [1] "Median expression (centered/weighted): -69.8240740740739"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:58 CEST"
## [1] "[40/50] Working on ESTROGEN_RESPONSE_EARLY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ESTROGEN_RESPONSE_EARLY"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "STC2" "BCL2" "TMPRSS3" "CBFA2T3" "SNX24" "SEC14L2" "INHBB"
## [8] "CALB2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.18885529897132 L1/L2 = 3.04646834746053"
## [1] "Median expression (uncentered): 10966"
## [1] "Median expression (centered/weighted): -92.0462962962965"
## [1] "Post-filter data"
## [1] "L1 = 0.153579523138073 L1/L2 = 2.34861459501229"
## [1] "Median expression (uncentered): 11058"
## [1] "Median expression (centered/weighted): -73.7962962962965"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:03:59 CEST"
## [1] "[41/50] Working on ESTROGEN_RESPONSE_LATE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ESTROGEN_RESPONSE_LATE"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "TMPRSS3" "BCL2" "GLA" "KIF20A" "PRKAR2B"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.166672550253525 L1/L2 = 2.60902758651494"
## [1] "Median expression (uncentered): 11141"
## [1] "Median expression (centered/weighted): -79.1574074074074"
## [1] "Post-filter data"
## [1] "L1 = 0.142966094069391 L1/L2 = 2.17672421165461"
## [1] "Median expression (uncentered): 11163.5"
## [1] "Median expression (centered/weighted): -68.8703703703704"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:00 CEST"
## [1] "[42/50] Working on MYOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYOGENESIS"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "SSPN" "MB" "FKBP1B" "NCAM1" "STC2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.170391952737528 L1/L2 = 2.02573672557226"
## [1] "Median expression (uncentered): 8679.5"
## [1] "Median expression (centered/weighted): -135.5"
## [1] "Post-filter data"
## [1] "L1 = 0.140927605566373 L1/L2 = 1.61512015877728"
## [1] "Median expression (uncentered): 8677"
## [1] "Median expression (centered/weighted): -135.5"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:01 CEST"
## [1] "[43/50] Working on APICAL_JUNCTION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APICAL_JUNCTION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "11 genes will be filtered:"
## [1] "CDH3" "CLDN14" "CADM3" "CLDN8" "CALB2"
## [6] "VWF" "CD209" "NEGR1" "PLCG1" "TNFRSF11B"
## [11] "MADCAM1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.1815744362019 L1/L2 = 2.30365652944632"
## [1] "Median expression (uncentered): 10017"
## [1] "Median expression (centered/weighted): -158.259259259259"
## [1] "Post-filter data"
## [1] "L1 = 0.112145048962866 L1/L2 = 1.32105598046421"
## [1] "Median expression (uncentered): 10172.5"
## [1] "Median expression (centered/weighted): -158.259259259259"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:03 CEST"
## [1] "[44/50] Working on MTORC1_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MTORC1_SIGNALING"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "CCNF" "STC1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.199641032825659 L1/L2 = 3.21354057387552"
## [1] "Median expression (uncentered): 12131.5"
## [1] "Median expression (centered/weighted): -36.3888888888887"
## [1] "Post-filter data"
## [1] "L1 = 0.189787893035265 L1/L2 = 2.99300701206726"
## [1] "Median expression (uncentered): 12139"
## [1] "Median expression (centered/weighted): -36.0277777777774"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:04 CEST"
## [1] "[45/50] Working on EPITHELIAL_MESENCHYMAL_TRANSITION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "9 genes will be filtered:"
## [1] "COL11A1" "FAP" "COMP" "INHBA" "SFRP1" "SFRP4" "CTHRC1"
## [8] "NTM" "ADAM12"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.19273799475978 L1/L2 = 2.07219714898495"
## [1] "Median expression (uncentered): 11054"
## [1] "Median expression (centered/weighted): -154.425925925926"
## [1] "Post-filter data"
## [1] "L1 = 0.150751853079105 L1/L2 = 1.61536542512385"
## [1] "Median expression (uncentered): 11179.5"
## [1] "Median expression (centered/weighted): -108.175925925926"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:05 CEST"
## [1] "[46/50] Working on OXIDATIVE_PHOSPHORYLATION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_OXIDATIVE_PHOSPHORYLATION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "ATP5G3" "UQCRFS1" "ATP5F1" "ATP6V1C1" "CASP7"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.158068767530276 L1/L2 = 1.66766951720479"
## [1] "Median expression (uncentered): 13283.5"
## [1] "Median expression (centered/weighted): 115.425925925926"
## [1] "Post-filter data"
## [1] "L1 = 0.139926508978587 L1/L2 = 1.44952597397256"
## [1] "Median expression (uncentered): 13279.5"
## [1] "Median expression (centered/weighted): 113.462962962964"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:06 CEST"
## [1] "[47/50] Working on P53_PATHWAY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_P53_PATHWAY"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "RGS16" "PVT1" "INHBB" "FAM162A" "F2R" "KRT17" "LRMP"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.140988346868851 L1/L2 = 2.35116007386196"
## [1] "Median expression (uncentered): 11796"
## [1] "Median expression (centered/weighted): -68.0555555555554"
## [1] "Post-filter data"
## [1] "L1 = 0.112113719564432 L1/L2 = 1.86433721039821"
## [1] "Median expression (uncentered): 11851"
## [1] "Median expression (centered/weighted): -57.8611111111113"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:07 CEST"
## [1] "[48/50] Working on IL2_STAT5_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_IL2_STAT5_SIGNALING"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "PTGER2" "ITIH5" "IRF4" "RGS16" "BCL2" "PUS1" "ETV4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.172935331778029 L1/L2 = 2.33246263348887"
## [1] "Median expression (uncentered): 10871"
## [1] "Median expression (centered/weighted): -67.0277777777774"
## [1] "Post-filter data"
## [1] "L1 = 0.135278822840657 L1/L2 = 1.75223898580731"
## [1] "Median expression (uncentered): 10890.5"
## [1] "Median expression (centered/weighted): -66.7129629629626"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:09 CEST"
## [1] "[49/50] Working on ALLOGRAFT_REJECTION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ALLOGRAFT_REJECTION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "4 genes will be filtered:"
## [1] "CD3G" "IRF4" "IL16" "MAP4K1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.214531688750509 L1/L2 = 1.95393045001771"
## [1] "Median expression (uncentered): 10220"
## [1] "Median expression (centered/weighted): -36.8703703703704"
## [1] "Post-filter data"
## [1] "L1 = 0.192062488245483 L1/L2 = 1.6893674890151"
## [1] "Median expression (uncentered): 10251"
## [1] "Median expression (centered/weighted): -36.8703703703704"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:10 CEST"
## [1] "[50/50] Working on KRAS_SIGNALING_UP - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_KRAS_SIGNALING_UP"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "INHBA" "PRKG2" "ITGBL1" "NR0B2" "TMEM100" "CBX8" "HDAC9"
## [8] "ARG1" "RGS16" "TPH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.174118776052847 L1/L2 = 2.11418211046724"
## [1] "Median expression (uncentered): 10763"
## [1] "Median expression (centered/weighted): -75.1759259259261"
## [1] "Post-filter data"
## [1] "L1 = 0.127941965247088 L1/L2 = 1.48391546665596"
## [1] "Median expression (uncentered): 10880.5"
## [1] "Median expression (centered/weighted): -50.7962962962956"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
tictoc::toc()
## 264.597 sec elapsed
and with fixed center
tictoc::tic()
Data.FC <- rRoma.R(ExpressionMatrix = MatData, centerData = TRUE, ExpFilter = FALSE,
ApproxSamples = 5, ModuleList = AllHall, MinGenes = 10,
MaxGenes = 200, nSamples = 100, UseWeigths = FALSE,
DefaultWeight = 1, FixedCenter = TRUE,
GeneOutDetection = 'L1OutExpOut', GeneOutThr = 5,
GeneSelMode = "All", SampleFilter = TRUE, MoreInfo = FALSE,
PlotData = FALSE, PCSignMode = "CorrelateAllWeightsByGene", OutGeneNumber = 5,
Ncomp = 100, OutGeneSpace = 5, PCADims = 2, PCSignThr = NULL,
UseParallel = TRUE, nCores = 3, ClusType = "FORK", FullSampleInfo = FALSE)
## [1] "Centering gene expression over samples"
## [1] "Using global center (centering over genes)"
## [1] "All the genesets will be used"
## [1] "2017-04-12 17:04:12 CEST"
## [1] "[1/50] Working on NOTCH_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_NOTCH_SIGNALING"
## [1] "32 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "KAT2A"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.219873583030237 L1/L2 = 2.15379598282959"
## [1] "Median expression (uncentered): 11705.5"
## [1] "Median expression (centered/weighted): -45.7034326356486"
## [1] "Post-filter data"
## [1] "L1 = 0.201513622653755 L1/L2 = 1.88344421672319"
## [1] "Median expression (uncentered): 11760.5"
## [1] "Median expression (centered/weighted): -8.17293550944277"
## [1] "Previous sample size: 0"
## [1] "Next sample size: 32"
## [1] "Computing samples"
## user system elapsed
## 0.052 0.032 2.276
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:14 CEST"
## [1] "[2/50] Working on HEDGEHOG_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HEDGEHOG_SIGNALING"
## [1] "36 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "SHH" "SCG2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.239271254081106 L1/L2 = 2.16614792723155"
## [1] "Median expression (uncentered): 9107"
## [1] "Median expression (centered/weighted): -200.467419432112"
## [1] "Post-filter data"
## [1] "L1 = 0.190274732841106 L1/L2 = 1.55771442361621"
## [1] "Median expression (uncentered): 9113"
## [1] "Median expression (centered/weighted): -204.349485128293"
## [1] "Previous sample size: 32"
## [1] "Next sample size: 36"
## [1] "Computing samples"
## user system elapsed
## 0.051 0.029 3.023
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:17 CEST"
## [1] "[3/50] Working on ANGIOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ANGIOGENESIS"
## [1] "36 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "SERPINA5" "OLR1" "CXCL6"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.244504105025021 L1/L2 = 2.11962339901147"
## [1] "Median expression (uncentered): 9486.5"
## [1] "Median expression (centered/weighted): -512.604901761469"
## [1] "Post-filter data"
## [1] "L1 = 0.183160892956892 L1/L2 = 1.58144087570602"
## [1] "Median expression (uncentered): 9866"
## [1] "Median expression (centered/weighted): -373.98062533194"
## [1] "Previous sample size: 36"
## [1] "Next sample size: 36"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:17 CEST"
## [1] "[4/50] Working on PANCREAS_BETA_CELLS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PANCREAS_BETA_CELLS"
## [1] "40 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "SST"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.430420018591429 L1/L2 = 5.28806444854772"
## [1] "Median expression (uncentered): 5991.5"
## [1] "Median expression (centered/weighted): -79.1841848337423"
## [1] "Post-filter data"
## [1] "L1 = 0.392559749618496 L1/L2 = 4.34872487569371"
## [1] "Median expression (uncentered): 5945"
## [1] "Median expression (centered/weighted): -76.0745953284883"
## [1] "Previous sample size: 36"
## [1] "Next sample size: 40"
## [1] "Computing samples"
## user system elapsed
## 0.054 0.029 2.869
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:20 CEST"
## [1] "[5/50] Working on WNT_BETA_CATENIN_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_WNT_BETA_CATENIN_SIGNALING"
## [1] "42 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.206342499798179 L1/L2 = 2.06388978657662"
## [1] "Median expression (uncentered): 10239"
## [1] "Median expression (centered/weighted): -316.587859145474"
## [1] "Post-filter data"
## [1] "L1 = 0.206342499798179 L1/L2 = 2.06388978657417"
## [1] "Median expression (uncentered): 10239"
## [1] "Median expression (centered/weighted): -316.587859145474"
## [1] "Previous sample size: 40"
## [1] "Next sample size: 42"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:20 CEST"
## [1] "[6/50] Working on APICAL_SURFACE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APICAL_SURFACE"
## [1] "44 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.273281977716708 L1/L2 = 3.1246539829877"
## [1] "Median expression (uncentered): 8648"
## [1] "Median expression (centered/weighted): -92.46104933281"
## [1] "Post-filter data"
## [1] "L1 = 0.273281977716708 L1/L2 = 3.12465398298766"
## [1] "Median expression (uncentered): 8648"
## [1] "Median expression (centered/weighted): -92.46104933281"
## [1] "Previous sample size: 40"
## [1] "Next sample size: 44"
## [1] "Computing samples"
## user system elapsed
## 0.059 0.032 3.207
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:24 CEST"
## [1] "[7/50] Working on REACTIVE_OXIGEN_SPECIES_PATHWAY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY"
## [1] "48 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.180597673563344 L1/L2 = 1.72744465247556"
## [1] "Median expression (uncentered): 12683.5"
## [1] "Median expression (centered/weighted): 3.62421339044671"
## [1] "Post-filter data"
## [1] "L1 = 0.180597673563344 L1/L2 = 1.72744465258943"
## [1] "Median expression (uncentered): 12683.5"
## [1] "Median expression (centered/weighted): 3.62421339044671"
## [1] "Previous sample size: 44"
## [1] "Next sample size: 48"
## [1] "Computing samples"
## user system elapsed
## 0.056 0.029 3.822
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:28 CEST"
## [1] "[8/50] Working on TGF_BETA_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TGF_BETA_SIGNALING"
## [1] "54 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.166735511876116 L1/L2 = 2.09284175767575"
## [1] "Median expression (uncentered): 12778"
## [1] "Median expression (centered/weighted): 102.305946791863"
## [1] "Post-filter data"
## [1] "L1 = 0.166735511876116 L1/L2 = 2.09284175767575"
## [1] "Median expression (uncentered): 12778"
## [1] "Median expression (centered/weighted): 102.305946791863"
## [1] "Previous sample size: 48"
## [1] "Next sample size: 54"
## [1] "Computing samples"
## user system elapsed
## 0.063 0.031 4.786
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:32 CEST"
## [1] "[9/50] Working on MYC_TARGETS_V2 - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYC_TARGETS_V2"
## [1] "58 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "0 genes will be filtered:"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.304155841973937 L1/L2 = 3.2569719236636"
## [1] "Median expression (uncentered): 11774.5"
## [1] "Median expression (centered/weighted): 21.4906016607644"
## [1] "Post-filter data"
## [1] "L1 = 0.304155841973936 L1/L2 = 3.25697192366359"
## [1] "Median expression (uncentered): 11774.5"
## [1] "Median expression (centered/weighted): 21.4906016607644"
## [1] "Previous sample size: 54"
## [1] "Next sample size: 58"
## [1] "Computing samples"
## user system elapsed
## 0.056 0.027 4.838
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:37 CEST"
## [1] "[10/50] Working on CHOLESTEROL_HOMEOSTASIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_CHOLESTEROL_HOMEOSTASIS"
## [1] "74 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "ADH4" "CTNNB1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.142226698768382 L1/L2 = 1.79472884000323"
## [1] "Median expression (uncentered): 12220"
## [1] "Median expression (centered/weighted): 14.1773289395088"
## [1] "Post-filter data"
## [1] "L1 = 0.126587040965931 L1/L2 = 1.57615541064143"
## [1] "Median expression (uncentered): 12324.5"
## [1] "Median expression (centered/weighted): 34.2818997457949"
## [1] "Previous sample size: 58"
## [1] "Next sample size: 74"
## [1] "Computing samples"
## user system elapsed
## 0.059 0.031 7.329
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:45 CEST"
## [1] "[11/50] Working on IL6_JAK_STAT3_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_IL6_JAK_STAT3_SIGNALING"
## [1] "87 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "CNTFR"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.143671123695292 L1/L2 = 1.16662206105578"
## [1] "Median expression (uncentered): 11083"
## [1] "Median expression (centered/weighted): -131.760068129489"
## [1] "Post-filter data"
## [1] "L1 = 0.136215993605291 L1/L2 = 1.07921852527621"
## [1] "Median expression (uncentered): 11113.5"
## [1] "Median expression (centered/weighted): -113.774950868914"
## [1] "Previous sample size: 74"
## [1] "Next sample size: 87"
## [1] "Computing samples"
## user system elapsed
## 0.068 0.033 10.341
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:04:56 CEST"
## [1] "[12/50] Working on PROTEIN_SECRETION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PROTEIN_SECRETION"
## [1] "96 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "AP2M1" "COG2" "SSPN"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.135059732346016 L1/L2 = 1.5288505544395"
## [1] "Median expression (uncentered): 11815.5"
## [1] "Median expression (centered/weighted): -87.5981065423534"
## [1] "Post-filter data"
## [1] "L1 = 0.125793544881306 L1/L2 = 1.37910200918196"
## [1] "Median expression (uncentered): 11817"
## [1] "Median expression (centered/weighted): -87.458848480837"
## [1] "Previous sample size: 87"
## [1] "Next sample size: 96"
## [1] "Computing samples"
## user system elapsed
## 0.080 0.036 11.639
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:08 CEST"
## [1] "[13/50] Working on INTERFERON_ALPHA_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INTERFERON_ALPHA_RESPONSE"
## [1] "97 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "SAMD9" "SAMD9L" "IL7"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.121907072531461 L1/L2 = 1.23105576668246"
## [1] "Median expression (uncentered): 11800.5"
## [1] "Median expression (centered/weighted): 35.0470393694825"
## [1] "Post-filter data"
## [1] "L1 = 0.105947937009135 L1/L2 = 1.08815481838268"
## [1] "Median expression (uncentered): 11815.5"
## [1] "Median expression (centered/weighted): 21.2983509763969"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 97"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:08 CEST"
## [1] "[14/50] Working on ANDROGEN_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ANDROGEN_RESPONSE"
## [1] "101 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "TARP" "KRT8" "PTPN21"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.174321285489668 L1/L2 = 2.13824063306666"
## [1] "Median expression (uncentered): 11686.5"
## [1] "Median expression (centered/weighted): -31.5228422116006"
## [1] "Post-filter data"
## [1] "L1 = 0.149993900956018 L1/L2 = 1.78205139090265"
## [1] "Median expression (uncentered): 11701.5"
## [1] "Median expression (centered/weighted): -17.9614646027667"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 101"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:08 CEST"
## [1] "[15/50] Working on PEROXISOME - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PEROXISOME"
## [1] "103 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "FABP6"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.179766663361789 L1/L2 = 2.34479966350732"
## [1] "Median expression (uncentered): 11493"
## [1] "Median expression (centered/weighted): 32.328654257423"
## [1] "Post-filter data"
## [1] "L1 = 0.167219138445514 L1/L2 = 2.20334916009573"
## [1] "Median expression (uncentered): 11515"
## [1] "Median expression (centered/weighted): 33.7702319995833"
## [1] "Previous sample size: 96"
## [1] "Next sample size: 103"
## [1] "Computing samples"
## user system elapsed
## 0.088 0.036 12.755
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:21 CEST"
## [1] "[16/50] Working on PI3K_AKT_MTOR_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_PI3K_AKT_MTOR_SIGNALING"
## [1] "105 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "4 genes will be filtered:"
## [1] "PLCG1" "CDK2" "PRKCB" "PITX2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181325962399155 L1/L2 = 2.26333139379507"
## [1] "Median expression (uncentered): 11434"
## [1] "Median expression (centered/weighted): -61.7983387625736"
## [1] "Post-filter data"
## [1] "L1 = 0.1499581552872 L1/L2 = 1.73972257891651"
## [1] "Median expression (uncentered): 11462.5"
## [1] "Median expression (centered/weighted): -61.2427832070188"
## [1] "Previous sample size: 103"
## [1] "Next sample size: 105"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:22 CEST"
## [1] "[17/50] Working on UNFOLDED_PROTEIN_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UNFOLDED_PROTEIN_RESPONSE"
## [1] "112 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "NOP14" "STC2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.216438543324013 L1/L2 = 3.38960853382172"
## [1] "Median expression (uncentered): 12035"
## [1] "Median expression (centered/weighted): -19.5499907805344"
## [1] "Post-filter data"
## [1] "L1 = 0.19032319750964 L1/L2 = 2.90373633940444"
## [1] "Median expression (uncentered): 12041"
## [1] "Median expression (centered/weighted): -19.5499907805344"
## [1] "Previous sample size: 103"
## [1] "Next sample size: 112"
## [1] "Computing samples"
## user system elapsed
## 0.107 0.043 15.903
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:38 CEST"
## [1] "[18/50] Working on BILE_ACID_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_BILE_ACID_METABOLISM"
## [1] "112 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "AKR1D1" "CYP8B1" "SLC27A5" "AGXT" "HAO1" "AQP9" "ALDH8A1"
## [8] "GNMT" "DIO1" "GC"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.278178767046406 L1/L2 = 2.57413569734681"
## [1] "Median expression (uncentered): 10112.5"
## [1] "Median expression (centered/weighted): -170.54844829298"
## [1] "Post-filter data"
## [1] "L1 = 0.178171996083482 L1/L2 = 1.56755491779576"
## [1] "Median expression (uncentered): 10704"
## [1] "Median expression (centered/weighted): -59.0177301359914"
## [1] "Previous sample size: 112"
## [1] "Next sample size: 112"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:38 CEST"
## [1] "[19/50] Working on SPERMATOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_SPERMATOGENESIS"
## [1] "133 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "24 genes will be filtered:"
## [1] "PHF7" "YBX2" "CSNK2A2" "MLF1" "HSPA2" "CLPB" "RPL39L"
## [8] "CHFR" "EZH2" "NEK2" "GMCL1" "MTNR1A" "DBF4" "PRKAR2A"
## [15] "TTK" "NCAPH" "PEBP1" "SCG5" "TLE4" "ACE" "STRBP"
## [22] "MEP1B" "GFI1" "IP6K1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.200765061265881 L1/L2 = 2.48280221884442"
## [1] "Median expression (uncentered): 5053"
## [1] "Median expression (centered/weighted): -81.1491374677517"
## [1] "Post-filter data"
## [1] "L1 = 0.175609850893134 L1/L2 = 1.80485695855858"
## [1] "Median expression (uncentered): 3502"
## [1] "Median expression (centered/weighted): -85.8884306735568"
## [1] "Previous sample size: 112"
## [1] "Next sample size: 133"
## [1] "Computing samples"
## user system elapsed
## 0.101 0.040 20.621
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:05:59 CEST"
## [1] "[20/50] Working on COAGULATION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_COAGULATION"
## [1] "137 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "18 genes will be filtered:"
## [1] "F2" "PLG" "F9" "PROZ" "F11" "MBL2"
## [7] "F13B" "MASP2" "C8A" "C8B" "C9" "SERPINC1"
## [13] "ITIH1" "KLKB1" "TF" "HRG" "CPN1" "CPB2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.327017538414526 L1/L2 = 3.18375816575241"
## [1] "Median expression (uncentered): 10678"
## [1] "Median expression (centered/weighted): -458.614802837389"
## [1] "Post-filter data"
## [1] "L1 = 0.194495485836815 L1/L2 = 1.90200076688214"
## [1] "Median expression (uncentered): 11361"
## [1] "Median expression (centered/weighted): -210.00950589967"
## [1] "Previous sample size: 133"
## [1] "Next sample size: 137"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:00 CEST"
## [1] "[21/50] Working on UV_RESPONSE_DN - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UV_RESPONSE_DN"
## [1] "144 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "LPAR1" "PTPN21" "PRKAR2B" "SERPINE1" "COL11A1" "KCNMA1"
## [7] "ATP2B1" "KIT"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.176647223034185 L1/L2 = 2.5992161383515"
## [1] "Median expression (uncentered): 11625.5"
## [1] "Median expression (centered/weighted): 28.9858335421495"
## [1] "Post-filter data"
## [1] "L1 = 0.122226785525289 L1/L2 = 1.78064559492199"
## [1] "Median expression (uncentered): 11672"
## [1] "Median expression (centered/weighted): 36.0876385086841"
## [1] "Previous sample size: 133"
## [1] "Next sample size: 144"
## [1] "Computing samples"
## user system elapsed
## 0.120 0.041 23.730
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:24 CEST"
## [1] "[22/50] Working on DNA_REPAIR - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_DNA_REPAIR"
## [1] "149 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "POLR2D" "RPA3" "TH1L" "FEN1" "CCNO"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.183076479671747 L1/L2 = 2.55349898167826"
## [1] "Median expression (uncentered): 12151.5"
## [1] "Median expression (centered/weighted): 2.4959264932773"
## [1] "Post-filter data"
## [1] "L1 = 0.152095239472454 L1/L2 = 2.00236126105211"
## [1] "Median expression (uncentered): 12176.5"
## [1] "Median expression (centered/weighted): 10.1965109443735"
## [1] "Previous sample size: 144"
## [1] "Next sample size: 149"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:25 CEST"
## [1] "[23/50] Working on FATTY_ACID_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_FATTY_ACID_METABOLISM"
## [1] "158 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "CYP4A11" "HAO2" "RDH16" "TDO2" "CPOX" "CEL"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181951901839269 L1/L2 = 2.358157876526"
## [1] "Median expression (uncentered): 11697"
## [1] "Median expression (centered/weighted): -35.4986178681129"
## [1] "Post-filter data"
## [1] "L1 = 0.155577662020637 L1/L2 = 2.32374119261239"
## [1] "Median expression (uncentered): 11791"
## [1] "Median expression (centered/weighted): -3.92710357478927"
## [1] "Previous sample size: 144"
## [1] "Next sample size: 158"
## [1] "Computing samples"
## user system elapsed
## 0.127 0.047 28.772
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:55 CEST"
## [1] "[24/50] Working on UV_RESPONSE_UP - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_UV_RESPONSE_UP"
## [1] "158 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "ATP6V1C1" "CDK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181524247141475 L1/L2 = 2.9234195566563"
## [1] "Median expression (uncentered): 11631"
## [1] "Median expression (centered/weighted): 0.24630827372274"
## [1] "Post-filter data"
## [1] "L1 = 0.170744520793088 L1/L2 = 2.70519300595409"
## [1] "Median expression (uncentered): 11631"
## [1] "Median expression (centered/weighted): 0.506126216851563"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 158"
## [1] "Reusing previous sampling (Same metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:55 CEST"
## [1] "[25/50] Working on APOPTOSIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APOPTOSIS"
## [1] "161 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "CDK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.169061406332043 L1/L2 = 2.83852024069534"
## [1] "Median expression (uncentered): 11603.5"
## [1] "Median expression (centered/weighted): -86.0462628067838"
## [1] "Post-filter data"
## [1] "L1 = 0.164561818338132 L1/L2 = 2.73576690045154"
## [1] "Median expression (uncentered): 11606.5"
## [1] "Median expression (centered/weighted): -84.7716208293737"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 161"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:06:56 CEST"
## [1] "[26/50] Working on ADIPOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ADIPOGENESIS"
## [1] "197 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "FABP4" "TST" "SSPN" "ITIH5" "SNCG" "DHRS7B"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.177454475935189 L1/L2 = 2.96983715731035"
## [1] "Median expression (uncentered): 11826.5"
## [1] "Median expression (centered/weighted): -74.2289358845251"
## [1] "Post-filter data"
## [1] "L1 = 0.153805699959167 L1/L2 = 2.56348962548956"
## [1] "Median expression (uncentered): 11837.5"
## [1] "Median expression (centered/weighted): -77.9602546463738"
## [1] "Previous sample size: 158"
## [1] "Next sample size: 197"
## [1] "Computing samples"
## user system elapsed
## 0.156 0.048 50.624
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:48 CEST"
## [1] "[27/50] Working on COMPLEMENT - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_COMPLEMENT"
## [1] "198 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "F5" "F7" "PLG" "KLKB1" "F2" "OLR1"
## [7] "C9" "SERPINC1" "APOA4" "ITIH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.179598713022695 L1/L2 = 2.17032037158722"
## [1] "Median expression (uncentered): 11150"
## [1] "Median expression (centered/weighted): -77.305672965847"
## [1] "Post-filter data"
## [1] "L1 = 0.137315612334335 L1/L2 = 1.59736808136481"
## [1] "Median expression (uncentered): 11345"
## [1] "Median expression (centered/weighted): -11.7012487254288"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 198"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:49 CEST"
## [1] "[28/50] Working on HEME_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HEME_METABOLISM"
## [1] "198 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "CPOX" "TRAK2" "KAT2B" "HDGF" "SLC30A10" "DARC"
## [7] "CDR2" "ABCG2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.196545460351494 L1/L2 = 3.06788980441999"
## [1] "Median expression (uncentered): 10907.5"
## [1] "Median expression (centered/weighted): -70.5332188385992"
## [1] "Post-filter data"
## [1] "L1 = 0.157168028300374 L1/L2 = 2.40801736088955"
## [1] "Median expression (uncentered): 10909.5"
## [1] "Median expression (centered/weighted): -70.2790838687719"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 198"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:50 CEST"
## [1] "[29/50] Working on MITOTIC_SPINDLE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MITOTIC_SPINDLE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "KIF23" "CKAP5" "TTK" "KIF4A" "ESPL1" "CENPF" "KIF20B"
## [8] "DLGAP5" "SMC1A" "SMC4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.19866788891322 L1/L2 = 1.97680360189143"
## [1] "Median expression (uncentered): 11343.5"
## [1] "Median expression (centered/weighted): -73.300051849645"
## [1] "Post-filter data"
## [1] "L1 = 0.158828619206203 L1/L2 = 1.69663433273335"
## [1] "Median expression (uncentered): 11373.5"
## [1] "Median expression (centered/weighted): -82.3400087781925"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:52 CEST"
## [1] "[30/50] Working on INTERFERON_GAMMA_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INTERFERON_GAMMA_RESPONSE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "CASP7" "KLRK1" "IL7" "SSPN" "IRF4" "P2RY14"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.148517814991739 L1/L2 = 1.51984882298382"
## [1] "Median expression (uncentered): 11584.5"
## [1] "Median expression (centered/weighted): 34.1945496409138"
## [1] "Post-filter data"
## [1] "L1 = 0.122281794347528 L1/L2 = 1.21060841552034"
## [1] "Median expression (uncentered): 11605"
## [1] "Median expression (centered/weighted): 36.8563961817225"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:53 CEST"
## [1] "[31/50] Working on E2F_TARGETS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_E2F_TARGETS"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "DSCC1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.318751903524161 L1/L2 = 3.85699915669839"
## [1] "Median expression (uncentered): 12250.5"
## [1] "Median expression (centered/weighted): -3.58416544922453"
## [1] "Post-filter data"
## [1] "L1 = 0.312445758063376 L1/L2 = 3.73637016863589"
## [1] "Median expression (uncentered): 12255.5"
## [1] "Median expression (centered/weighted): -2.54568560518338"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:54 CEST"
## [1] "[32/50] Working on MYC_TARGETS_V1 - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYC_TARGETS_V1"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "1 genes will be filtered:"
## [1] "SSBP1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.272828197451803 L1/L2 = 4.36026496708887"
## [1] "Median expression (uncentered): 13016"
## [1] "Median expression (centered/weighted): -56.2753472271473"
## [1] "Post-filter data"
## [1] "L1 = 0.267656673275935 L1/L2 = 4.22932906856006"
## [1] "Median expression (uncentered): 13016"
## [1] "Median expression (centered/weighted): -56.2753472271473"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:55 CEST"
## [1] "[33/50] Working on INFLAMMATORY_RESPONSE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_INFLAMMATORY_RESPONSE"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "AQP9" "INHBA" "BDKRB1" "OLR1" "PTGER2" "LPAR1" "RGS16"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.211647249996983 L1/L2 = 2.34840675368723"
## [1] "Median expression (uncentered): 9834.5"
## [1] "Median expression (centered/weighted): -111.924556401855"
## [1] "Post-filter data"
## [1] "L1 = 0.17992195079983 L1/L2 = 1.88435863441375"
## [1] "Median expression (uncentered): 9893"
## [1] "Median expression (centered/weighted): -105.270277308925"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:56 CEST"
## [1] "[34/50] Working on XENOBIOTIC_METABOLISM - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_XENOBIOTIC_METABOLISM"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "18 genes will be filtered:"
## [1] "CYP1A2" "FMO3" "SLC22A1" "ARG1" "UPB1" "HGFAC" "F11"
## [8] "GNMT" "GCKR" "PLG" "VTN" "HRG" "IGFBP1" "TAT"
## [15] "MBL2" "ANGPTL3" "CYP2E1" "ITIH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.295671948510834 L1/L2 = 3.81772303093792"
## [1] "Median expression (uncentered): 11196"
## [1] "Median expression (centered/weighted): -191.347800014814"
## [1] "Post-filter data"
## [1] "L1 = 0.171892500007753 L1/L2 = 1.98953433588045"
## [1] "Median expression (uncentered): 11514"
## [1] "Median expression (centered/weighted): -84.4602680421796"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:58 CEST"
## [1] "[35/50] Working on GLYCOLYSIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_GLYCOLYSIS"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "PRPS1" "NANP" "STC2" "STC1" "KIF20A" "CAPN5"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.189690836732643 L1/L2 = 2.9797940652477"
## [1] "Median expression (uncentered): 11560.5"
## [1] "Median expression (centered/weighted): -69.0481878627703"
## [1] "Post-filter data"
## [1] "L1 = 0.159988592387447 L1/L2 = 2.46683012829779"
## [1] "Median expression (uncentered): 11580"
## [1] "Median expression (centered/weighted): -60.7293322427572"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:07:59 CEST"
## [1] "[36/50] Working on KRAS_SIGNALING_DN - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_KRAS_SIGNALING_DN"
## [1] "199 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "17 genes will be filtered:"
## [1] "SPTBN2" "SIDT1" "CLDN8" "THRB" "SERPINA10"
## [6] "PRODH" "EDN2" "C5" "INSL5" "UGT2B17"
## [11] "SLC6A14" "YBX2" "GP2" "SLC38A3" "ITIH3"
## [16] "CNTFR" "SPHK2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.230838322553322 L1/L2 = 2.87834267664933"
## [1] "Median expression (uncentered): 3568"
## [1] "Median expression (centered/weighted): -167.054329445398"
## [1] "Post-filter data"
## [1] "L1 = 0.178452498408558 L1/L2 = 2.08567891422926"
## [1] "Median expression (uncentered): 3251.5"
## [1] "Median expression (centered/weighted): -153.113282807509"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 199"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:01 CEST"
## [1] "[37/50] Working on TNFA_SIGNALING_VIA_NFKB - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_TNFA_SIGNALING_VIA_NFKB"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "FOSL1" "SERPINE1" "TNFAIP6" "INHBA" "OLR1" "FJX1"
## [7] "DUSP4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.163683557948457 L1/L2 = 2.64533245268025"
## [1] "Median expression (uncentered): 11567.5"
## [1] "Median expression (centered/weighted): -18.1664176622905"
## [1] "Post-filter data"
## [1] "L1 = 0.131939936531859 L1/L2 = 2.0213883891778"
## [1] "Median expression (uncentered): 11665.5"
## [1] "Median expression (centered/weighted): 8.08740881002724"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:02 CEST"
## [1] "[38/50] Working on HYPOXIA - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_HYPOXIA"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "9 genes will be filtered:"
## [1] "SERPINE1" "STC1" "STC2" "KLF7" "B4GALNT2" "PPARGC1A"
## [7] "BCL2" "GCNT2" "SRPX"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.192927521891941 L1/L2 = 3.35554931122151"
## [1] "Median expression (uncentered): 11261"
## [1] "Median expression (centered/weighted): -150.480244733479"
## [1] "Post-filter data"
## [1] "L1 = 0.147398896812481 L1/L2 = 2.49260765987737"
## [1] "Median expression (uncentered): 11309"
## [1] "Median expression (centered/weighted): -147.128496896113"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:03 CEST"
## [1] "[39/50] Working on G2M_CHECKPOINT - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_G2M_CHECKPOINT"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "KIF4A" "ORC6"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.295014363478126 L1/L2 = 3.45004940867449"
## [1] "Median expression (uncentered): 11853"
## [1] "Median expression (centered/weighted): -110.500442061568"
## [1] "Post-filter data"
## [1] "L1 = 0.281376871158405 L1/L2 = 3.22150500710613"
## [1] "Median expression (uncentered): 11853.5"
## [1] "Median expression (centered/weighted): -110.500442061568"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:05 CEST"
## [1] "[40/50] Working on ESTROGEN_RESPONSE_EARLY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ESTROGEN_RESPONSE_EARLY"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "STC2" "BCL2" "TMPRSS3" "CBFA2T3" "SNX24" "SEC14L2" "INHBB"
## [8] "CALB2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.190074288220779 L1/L2 = 3.074596311535"
## [1] "Median expression (uncentered): 10966"
## [1] "Median expression (centered/weighted): -108.380539362391"
## [1] "Post-filter data"
## [1] "L1 = 0.154556005199807 L1/L2 = 2.37710786825814"
## [1] "Median expression (uncentered): 11058"
## [1] "Median expression (centered/weighted): -90.4791624312284"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:06 CEST"
## [1] "[41/50] Working on ESTROGEN_RESPONSE_LATE - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ESTROGEN_RESPONSE_LATE"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "4 genes will be filtered:"
## [1] "TMPRSS3" "BCL2" "KIF20A" "PRKAR2B"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.167764884802528 L1/L2 = 2.683421747033"
## [1] "Median expression (uncentered): 11141"
## [1] "Median expression (centered/weighted): -101.225483312767"
## [1] "Post-filter data"
## [1] "L1 = 0.146908184454418 L1/L2 = 2.3077159440854"
## [1] "Median expression (uncentered): 11164.5"
## [1] "Median expression (centered/weighted): -95.0766870440504"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:07 CEST"
## [1] "[42/50] Working on MYOGENESIS - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MYOGENESIS"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "6 genes will be filtered:"
## [1] "SSPN" "MB" "BDKRB2" "FKBP1B" "NCAM1" "STC2"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.169729361569857 L1/L2 = 2.09076220021458"
## [1] "Median expression (uncentered): 8679.5"
## [1] "Median expression (centered/weighted): -152.101008310127"
## [1] "Post-filter data"
## [1] "L1 = 0.137069796038296 L1/L2 = 1.61670492631858"
## [1] "Median expression (uncentered): 8667.5"
## [1] "Median expression (centered/weighted): -151.416561470198"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:08 CEST"
## [1] "[43/50] Working on APICAL_JUNCTION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_APICAL_JUNCTION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "11 genes will be filtered:"
## [1] "CDH3" "CLDN14" "CADM3" "CLDN8" "CALB2"
## [6] "VWF" "CD209" "NEGR1" "PLCG1" "TNFRSF11B"
## [11] "MADCAM1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.181029321885175 L1/L2 = 2.32990698593197"
## [1] "Median expression (uncentered): 10017"
## [1] "Median expression (centered/weighted): -184.266254233468"
## [1] "Post-filter data"
## [1] "L1 = 0.112682745003074 L1/L2 = 1.35978256994535"
## [1] "Median expression (uncentered): 10172.5"
## [1] "Median expression (centered/weighted): -176.042293314548"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:09 CEST"
## [1] "[44/50] Working on MTORC1_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_MTORC1_SIGNALING"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "2 genes will be filtered:"
## [1] "CCNF" "STC1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.201001123527623 L1/L2 = 3.16363966507818"
## [1] "Median expression (uncentered): 12131.5"
## [1] "Median expression (centered/weighted): -46.6012734682691"
## [1] "Post-filter data"
## [1] "L1 = 0.190889836109695 L1/L2 = 2.94378220627342"
## [1] "Median expression (uncentered): 12139"
## [1] "Median expression (centered/weighted): -46.4432833433415"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:10 CEST"
## [1] "[45/50] Working on EPITHELIAL_MESENCHYMAL_TRANSITION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "8 genes will be filtered:"
## [1] "COL11A1" "FAP" "COMP" "INHBA" "SFRP1" "SFRP4" "CTHRC1"
## [8] "ADAM12"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.194156945307458 L1/L2 = 2.17395732455097"
## [1] "Median expression (uncentered): 11054"
## [1] "Median expression (centered/weighted): -170.129475183877"
## [1] "Post-filter data"
## [1] "L1 = 0.154891473141009 L1/L2 = 1.69277282057833"
## [1] "Median expression (uncentered): 11167"
## [1] "Median expression (centered/weighted): -130.79419118493"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:11 CEST"
## [1] "[46/50] Working on OXIDATIVE_PHOSPHORYLATION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_OXIDATIVE_PHOSPHORYLATION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "5 genes will be filtered:"
## [1] "ATP5G3" "UQCRFS1" "ATP5F1" "ATP6V1C1" "CASP7"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.15837091153834 L1/L2 = 1.69247206506322"
## [1] "Median expression (uncentered): 13283.5"
## [1] "Median expression (centered/weighted): 113.776607614806"
## [1] "Post-filter data"
## [1] "L1 = 0.138943620993485 L1/L2 = 1.44077434888217"
## [1] "Median expression (uncentered): 13279.5"
## [1] "Median expression (centered/weighted): 111.364575896692"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:12 CEST"
## [1] "[47/50] Working on P53_PATHWAY - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_P53_PATHWAY"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "RGS16" "PVT1" "INHBB" "FAM162A" "F2R" "KRT17" "LRMP"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.142232441521843 L1/L2 = 2.39776868243571"
## [1] "Median expression (uncentered): 11796"
## [1] "Median expression (centered/weighted): -72.3813651743748"
## [1] "Post-filter data"
## [1] "L1 = 0.11290632294424 L1/L2 = 1.89083562052079"
## [1] "Median expression (uncentered): 11851"
## [1] "Median expression (centered/weighted): -65.1271001864385"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:14 CEST"
## [1] "[48/50] Working on IL2_STAT5_SIGNALING - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_IL2_STAT5_SIGNALING"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "7 genes will be filtered:"
## [1] "PTGER2" "ITIH5" "IRF4" "RGS16" "BCL2" "PUS1" "ETV4"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.173697206752815 L1/L2 = 2.46039429101391"
## [1] "Median expression (uncentered): 10871"
## [1] "Median expression (centered/weighted): -88.6811558058203"
## [1] "Post-filter data"
## [1] "L1 = 0.136442288901935 L1/L2 = 1.85969322688518"
## [1] "Median expression (uncentered): 10890.5"
## [1] "Median expression (centered/weighted): -88.242237130965"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:15 CEST"
## [1] "[49/50] Working on ALLOGRAFT_REJECTION - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_ALLOGRAFT_REJECTION"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "3 genes will be filtered:"
## [1] "IRF4" "IL16" "MAP4K1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.21235767353146 L1/L2 = 1.95760094162477"
## [1] "Median expression (uncentered): 10220"
## [1] "Median expression (centered/weighted): -86.2337378866463"
## [1] "Post-filter data"
## [1] "L1 = 0.193770338766319 L1/L2 = 1.73798636605109"
## [1] "Median expression (uncentered): 10243.5"
## [1] "Median expression (centered/weighted): -85.1116319715315"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "2017-04-12 17:08:16 CEST"
## [1] "[50/50] Working on KRAS_SIGNALING_UP - http://www.broadinstitute.org/gsea/msigdb/cards/HALLMARK_KRAS_SIGNALING_UP"
## [1] "200 genes available for analysis"
## [1] "Detecting outliers using leave one out and median-absolute-deviations away from median (scater package)"
## [1] "10 genes will be filtered:"
## [1] "INHBA" "PRKG2" "ITGBL1" "NR0B2" "TMEM100" "CBX8" "HDAC9"
## [8] "ARG1" "RGS16" "TPH1"
## [1] "Not using weigths for PCA computation"
## [1] "Pre-filter data"
## [1] "L1 = 0.176272116490085 L1/L2 = 2.18494512858741"
## [1] "Median expression (uncentered): 10763"
## [1] "Median expression (centered/weighted): -56.9704583098913"
## [1] "Post-filter data"
## [1] "L1 = 0.129180793012456 L1/L2 = 1.5341744194258"
## [1] "Median expression (uncentered): 10880.5"
## [1] "Median expression (centered/weighted): -32.5770341529995"
## [1] "Previous sample size: 197"
## [1] "Next sample size: 200"
## [1] "Reusing previous sampling (Comparable metagene size)"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
## [1] "Missing gene weights will be replaced by 1"
## [1] "Orienting PC by correlating gene expression and PC projections"
## [1] "Not using groups"
## [1] "Computing correlations"
## [1] "Correcting using weights"
tictoc::toc()
## 245.652 sec elapsed
Let us have a look at the overdispersed genesets for using the fixed center
Plot.Genesets(RomaData = Data.FC,
Selected = SelectGeneSets(RomaData = Data.FC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
GenesetMargin = 20, SampleMargin = 14, cluster_cols = FALSE,
GroupInfo = Type, AggByGroupsFL = c("mean", "sd"))
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "17 geneset selected"
## $mean
## metastasized normal primary
## G2M_CHECKPOINT 13785.508 -20413.033 6627.5255
## APICAL_SURFACE -7738.800 10460.695 -2721.8952
## UNFOLDED_PROTEIN_RESPONSE 7841.244 -13529.012 5687.7681
## MTORC1_SIGNALING 12642.476 -19845.281 7202.8049
## E2F_TARGETS 15313.568 -23590.607 8277.0388
## MYC_TARGETS_V1 14284.996 -20718.122 6433.1259
## MYC_TARGETS_V2 -9619.450 14217.635 -4598.1853
## INFLAMMATORY_RESPONSE 15156.503 -20641.783 5485.2797
## XENOBIOTIC_METABOLISM 19898.967 -16185.878 -3713.0887
## GLYCOLYSIS 12925.198 -17151.324 4226.1260
## UV_RESPONSE_UP 11039.279 -16000.278 4960.9984
## COAGULATION 14924.172 -17410.229 2486.0570
## BILE_ACID_METABOLISM 13434.440 -14181.731 747.2908
## ALLOGRAFT_REJECTION -12137.469 19544.946 -7407.4772
## SPERMATOGENESIS -5371.171 8774.957 -3403.7868
## KRAS_SIGNALING_DN -9934.822 14541.299 -4606.4770
## PANCREAS_BETA_CELLS -12253.241 11697.670 555.5707
##
## $sd
## metastasized normal primary
## G2M_CHECKPOINT 15909.912 9773.904 22324.754
## APICAL_SURFACE 5904.758 4390.819 7660.033
## UNFOLDED_PROTEIN_RESPONSE 7440.740 6223.996 10487.014
## MTORC1_SIGNALING 10031.331 9909.728 14171.153
## E2F_TARGETS 17112.423 9106.418 24628.968
## MYC_TARGETS_V1 13465.119 6802.267 19603.864
## MYC_TARGETS_V2 8285.078 4539.072 12935.870
## INFLAMMATORY_RESPONSE 12384.577 8269.455 11295.247
## XENOBIOTIC_METABOLISM 12799.583 4685.762 8508.973
## GLYCOLYSIS 9263.295 8919.712 13296.602
## UV_RESPONSE_UP 8972.849 6247.225 11824.666
## COAGULATION 10792.014 7608.917 10649.475
## BILE_ACID_METABOLISM 9319.491 5307.929 7890.818
## ALLOGRAFT_REJECTION 13348.797 11897.710 14445.890
## SPERMATOGENESIS 7077.844 4729.878 8491.171
## KRAS_SIGNALING_DN 8842.913 4112.040 10589.546
## PANCREAS_BETA_CELLS 9014.235 2889.552 8421.746
and without the fixed center
Plot.Genesets(RomaData = Data.NFC,
Selected = SelectGeneSets(RomaData = Data.NFC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
GenesetMargin = 20, SampleMargin = 14, cluster_cols = FALSE,
GroupInfo = Type, AggByGroupsFL = c("mean", "sd"))
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "19 geneset selected"
## $mean
## metastasized normal primary
## MITOTIC_SPINDLE -10666.424 15928.28 -5261.8522
## G2M_CHECKPOINT 13541.345 -20235.22 6693.8759
## APOPTOSIS -10912.399 17269.83 -6357.4289
## ADIPOGENESIS -11172.030 18261.72 -7089.6911
## APICAL_SURFACE -7815.792 10497.93 -2682.1354
## UNFOLDED_PROTEIN_RESPONSE 7739.371 -13496.03 5756.6633
## MTORC1_SIGNALING 12636.750 -19838.35 7201.6031
## E2F_TARGETS 15185.880 -23508.01 8322.1279
## MYC_TARGETS_V1 14299.203 -20698.31 6399.1030
## MYC_TARGETS_V2 -9695.481 14256.39 -4560.9110
## INFLAMMATORY_RESPONSE 15248.574 -20898.06 5649.4812
## XENOBIOTIC_METABOLISM 19761.148 -16125.42 -3635.7255
## GLYCOLYSIS 12720.973 -16929.61 4208.6338
## UV_RESPONSE_UP 10614.442 -15776.05 5161.6051
## HEME_METABOLISM -11270.751 16569.54 -5298.7921
## COAGULATION 14707.638 -17285.26 2577.6254
## ALLOGRAFT_REJECTION -11914.849 19095.95 -7181.1049
## KRAS_SIGNALING_DN -10873.553 14855.54 -3981.9853
## PANCREAS_BETA_CELLS -11720.248 10850.21 870.0343
##
## $sd
## metastasized normal primary
## MITOTIC_SPINDLE 8154.292 10046.119 13710.795
## G2M_CHECKPOINT 16062.735 9892.127 22163.554
## APOPTOSIS 10215.670 9030.688 12032.194
## ADIPOGENESIS 9597.807 6504.970 11873.657
## APICAL_SURFACE 6020.690 4323.165 7774.129
## UNFOLDED_PROTEIN_RESPONSE 7349.409 6292.189 10330.097
## MTORC1_SIGNALING 10017.066 9943.920 14142.332
## E2F_TARGETS 17102.660 9146.348 24519.272
## MYC_TARGETS_V1 13466.089 6834.957 19576.709
## MYC_TARGETS_V2 8308.325 4530.718 13015.588
## INFLAMMATORY_RESPONSE 12532.583 8453.253 11458.803
## XENOBIOTIC_METABOLISM 12918.439 4667.232 8494.077
## GLYCOLYSIS 9096.323 9108.451 13028.355
## UV_RESPONSE_UP 8651.344 6322.760 11586.756
## HEME_METABOLISM 9717.573 8027.408 10424.115
## COAGULATION 11071.468 7675.294 10687.153
## ALLOGRAFT_REJECTION 13837.436 11983.868 14734.158
## KRAS_SIGNALING_DN 8681.709 3940.863 10440.061
## PANCREAS_BETA_CELLS 8272.596 3565.561 7825.787
Now we can look at the underdispersed geneset with fixed center
Plot.Genesets(RomaData = Data.FC,
Selected = SelectGeneSets(RomaData = Data.FC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Under",
MedThr = 1e-3, MedMode = "Wil", MedType = "Over"),
GenesetMargin = 20, SampleMargin = 14, cluster_cols = FALSE,
GroupInfo = Type, AggByGroupsFL = c("mean", "sd"))
## [1] "Using genestes underdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "Using genestes overdispersed according to Wilcoxon test. MedThr = 0.001"
## [1] "24 geneset selected"
## $mean
## metastasized normal primary
## TNFA_SIGNALING_VIA_NFKB 11065.927 -16208.882 5142.9560
## CHOLESTEROL_HOMEOSTASIS 7594.891 -9203.928 1609.0371
## WNT_BETA_CATENIN_SIGNALING -6579.438 10023.457 -3444.0190
## TGF_BETA_SIGNALING 6637.445 -9730.455 3093.0099
## IL6_JAK_STAT3_SIGNALING 8267.370 -11262.818 2995.4479
## DNA_REPAIR 8655.890 -13250.936 4595.0460
## NOTCH_SIGNALING 4658.829 -7989.595 3330.7661
## ANDROGEN_RESPONSE -9448.004 11952.938 -2504.9343
## MYOGENESIS -12475.646 16333.113 -3857.4666
## PROTEIN_SECRETION -5660.868 7251.382 -1590.5140
## INTERFERON_ALPHA_RESPONSE -2267.376 1722.863 544.5122
## INTERFERON_GAMMA_RESPONSE -10986.264 16722.658 -5736.3934
## APICAL_JUNCTION -10438.417 13512.080 -3073.6639
## HEDGEHOG_SIGNALING -7120.953 9550.341 -2429.3877
## COMPLEMENT -11412.056 16489.967 -5077.9111
## PI3K_AKT_MTOR_SIGNALING -7307.419 11502.897 -4195.4781
## FATTY_ACID_METABOLISM -12042.330 16760.797 -4718.4671
## OXIDATIVE_PHOSPHORYLATION -8906.093 14724.969 -5818.8766
## REACTIVE_OXIGEN_SPECIES_PATHWAY -5656.241 7928.593 -2272.3521
## P53_PATHWAY 8614.367 -13830.666 5216.2996
## UV_RESPONSE_DN -8595.896 11636.536 -3040.6400
## ANGIOGENESIS 6635.519 -7767.302 1131.7832
## IL2_STAT5_SIGNALING -12514.763 15978.986 -3464.2230
## KRAS_SIGNALING_UP -14066.112 17360.331 -3294.2198
##
## $sd
## metastasized normal primary
## TNFA_SIGNALING_VIA_NFKB 13563.813 8266.945 11122.153
## CHOLESTEROL_HOMEOSTASIS 7778.269 6434.568 6427.924
## WNT_BETA_CATENIN_SIGNALING 6908.742 5272.883 6865.613
## TGF_BETA_SIGNALING 6770.590 4606.674 7631.761
## IL6_JAK_STAT3_SIGNALING 6890.916 5592.974 6203.598
## DNA_REPAIR 7926.856 7438.795 9846.976
## NOTCH_SIGNALING 4609.071 5891.419 6586.098
## ANDROGEN_RESPONSE 6317.898 5292.988 8336.334
## MYOGENESIS 8898.440 5377.540 11551.169
## PROTEIN_SECRETION 6821.272 7319.716 7792.509
## INTERFERON_ALPHA_RESPONSE 12748.990 8973.108 9712.751
## INTERFERON_GAMMA_RESPONSE 9647.228 9665.503 10923.640
## APICAL_JUNCTION 7081.723 8013.011 10020.587
## HEDGEHOG_SIGNALING 5706.727 3039.034 5721.747
## COMPLEMENT 10063.203 9565.963 9713.688
## PI3K_AKT_MTOR_SIGNALING 6785.617 6017.923 7994.513
## FATTY_ACID_METABOLISM 9639.507 6317.881 10036.722
## OXIDATIVE_PHOSPHORYLATION 7584.350 7337.690 12358.733
## REACTIVE_OXIGEN_SPECIES_PATHWAY 5708.250 5383.546 7106.662
## P53_PATHWAY 8047.851 7175.915 12191.925
## UV_RESPONSE_DN 6985.977 9729.787 7769.214
## ANGIOGENESIS 7117.224 3456.384 5790.110
## IL2_STAT5_SIGNALING 9648.339 6511.449 10954.314
## KRAS_SIGNALING_UP 9533.261 6236.828 10318.642
and without the fixed center
Plot.Genesets(RomaData = Data.NFC,
Selected = SelectGeneSets(RomaData = Data.NFC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Under",
MedThr = 1e-3, MedMode = "Wil", MedType = "Over"),
GenesetMargin = 20, SampleMargin = 14, cluster_cols = FALSE,
GroupInfo = Type, AggByGroupsFL = c("mean", "sd"))
## [1] "Using genestes underdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "Using genestes overdispersed according to Wilcoxon test. MedThr = 0.001"
## [1] "26 geneset selected"
## $mean
## metastasized normal primary
## TNFA_SIGNALING_VIA_NFKB 10870.207 -16026.072 5155.8643
## HYPOXIA 13703.807 -16857.090 3153.2825
## CHOLESTEROL_HOMEOSTASIS 7555.301 -9179.659 1624.3584
## WNT_BETA_CATENIN_SIGNALING -6656.161 10038.805 -3382.6441
## TGF_BETA_SIGNALING 6588.444 -9698.415 3109.9706
## IL6_JAK_STAT3_SIGNALING -1394.279 4983.483 -3589.2043
## DNA_REPAIR 8131.778 -12638.329 4506.5510
## NOTCH_SIGNALING 4604.888 -7957.892 3353.0040
## ESTROGEN_RESPONSE_LATE -13170.979 18359.073 -5188.0939
## ANDROGEN_RESPONSE -9391.822 11914.696 -2522.8736
## MYOGENESIS -13226.629 16531.320 -3304.6912
## PROTEIN_SECRETION -5723.915 7303.488 -1579.5732
## INTERFERON_ALPHA_RESPONSE -5910.988 8392.363 -2481.3750
## INTERFERON_GAMMA_RESPONSE -10585.848 15937.151 -5351.3024
## APICAL_JUNCTION -10686.702 13617.306 -2930.6034
## HEDGEHOG_SIGNALING -7198.371 9578.529 -2380.1577
## COMPLEMENT -11405.921 16531.566 -5125.6448
## PI3K_AKT_MTOR_SIGNALING -7409.568 11535.540 -4125.9721
## OXIDATIVE_PHOSPHORYLATION -9376.932 15001.316 -5624.3838
## REACTIVE_OXIGEN_SPECIES_PATHWAY -5697.635 7925.462 -2227.8271
## P53_PATHWAY 8585.461 -13788.134 5202.6736
## UV_RESPONSE_DN -9667.912 13499.907 -3831.9944
## ANGIOGENESIS 8030.614 -8591.425 560.8117
## IL2_STAT5_SIGNALING -12630.765 16044.103 -3413.3386
## PEROXISOME -11666.161 13124.131 -1457.9704
## KRAS_SIGNALING_UP -14166.979 17388.466 -3221.4867
##
## $sd
## metastasized normal primary
## TNFA_SIGNALING_VIA_NFKB 14015.604 8341.323 11062.238
## HYPOXIA 10918.219 9116.951 10635.324
## CHOLESTEROL_HOMEOSTASIS 7818.803 6440.219 6436.654
## WNT_BETA_CATENIN_SIGNALING 6881.802 5271.283 6888.433
## TGF_BETA_SIGNALING 6825.701 4608.793 7654.583
## IL6_JAK_STAT3_SIGNALING 12414.985 8101.420 8390.342
## DNA_REPAIR 7989.435 6945.050 9143.200
## NOTCH_SIGNALING 4676.330 5915.346 6586.677
## ESTROGEN_RESPONSE_LATE 10117.333 8295.334 13440.823
## ANDROGEN_RESPONSE 6291.625 5343.384 8472.418
## MYOGENESIS 9477.304 4935.483 11824.482
## PROTEIN_SECRETION 6854.114 7285.430 7778.602
## INTERFERON_ALPHA_RESPONSE 11503.481 5512.454 9483.840
## INTERFERON_GAMMA_RESPONSE 10709.374 9743.894 11180.490
## APICAL_JUNCTION 7232.975 7607.489 10010.941
## HEDGEHOG_SIGNALING 5782.363 3048.111 5786.108
## COMPLEMENT 9959.564 9581.479 10004.276
## PI3K_AKT_MTOR_SIGNALING 6790.219 5984.390 8081.306
## OXIDATIVE_PHOSPHORYLATION 7521.892 7271.447 12166.338
## REACTIVE_OXIGEN_SPECIES_PATHWAY 5833.089 5314.996 7220.380
## P53_PATHWAY 8062.922 7231.575 12168.643
## UV_RESPONSE_DN 7751.143 8702.268 8691.015
## ANGIOGENESIS 7704.815 2832.390 5358.790
## IL2_STAT5_SIGNALING 9453.748 6496.228 11064.114
## PEROXISOME 8344.533 5334.308 8491.908
## KRAS_SIGNALING_UP 9372.167 6180.617 10518.605
We can also explore the gene weigths with the fixed center
PlotGeneWeight(RomaData = Data.FC, PlotGenes = 30,
ExpressionMatrix = MatData, LogExpression = FALSE,
Selected = SelectGeneSets(RomaData = Data.FC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
PlotWeigthSign = TRUE)
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "17 geneset selected"
and without the fixed center
PlotGeneWeight(RomaData = Data.NFC, PlotGenes = 30,
ExpressionMatrix = MatData, LogExpression = FALSE,
Selected = SelectGeneSets(RomaData = Data.NFC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
PlotWeigthSign = TRUE)
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "19 geneset selected"
Moreover, we can look at the projections of the samples with the fixed center
PlotSampleProjections(RomaData = Data.FC, PlotSamples = 30,
ExpressionMatrix = MatData, LogExpression = FALSE,
Selected = SelectGeneSets(RomaData = Data.FC, VarThr = 1e-6,
VarMode = "Wil", VarType = "Over"),
PlotPCProj = "none")
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 1e-06"
## [1] "15 geneset selected"
## NULL
and without the fixed center
PlotSampleProjections(RomaData = Data.NFC, PlotSamples = 30,
ExpressionMatrix = MatData, LogExpression = FALSE,
Selected = SelectGeneSets(RomaData = Data.NFC, VarThr = 1e-6,
VarMode = "Wil", VarType = "Over"),
PlotPCProj = "none")
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 1e-06"
## [1] "14 geneset selected"
## NULL
Additionaly, we can compare across samples
CompareAcrossSamples(RomaData = Data.FC,
Selected = SelectGeneSets(RomaData = Data.FC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
Groups = Type)
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "17 geneset selected"
## [1] "Performing Type III AOV (R default)"
## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 2.548e+10 1.274e+10 52.2 <2e-16 ***
## Residuals 915 2.233e+11 2.441e+08
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "A significant difference is observed across groups"
## [1] "Calculating Tukey Honest Significant Differences"
## [1] "3 significant differences found"
## [1] "Performing Type III AOV (R default)"
## Df Sum Sq Mean Sq F value Pr(>F)
## Group 2 2.548e+10 1.274e+10 106.00 <2e-16 ***
## Group:GeneSet 48 1.191e+11 2.482e+09 20.65 <2e-16 ***
## Residuals 867 1.042e+11 1.202e+08
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "A significant difference is observed across groups and metagenes"
## [1] "Calculating Tukey Honest Significant Differences"
## [1] "567 significant differences found"
Finally, we can look at genes which appear across different genesests and explore thier weithgs
PlotRecurringGenes(RomaData = Data.NFC,
Selected = SelectGeneSets(RomaData = Data.NFC, VarThr = 1e-3,
VarMode = "Wil", VarType = "Over"),
GenesByGroup = 25, MinMult = 3)
## [1] "Using genestes overdispersed according to Wilcoxon test. VarThr = 0.001"
## [1] "19 geneset selected"